Many autoimmune diseases exhibit familial aggregation, indicating that they have genetic determinants. Single nucleotide polymorphisms in PTPN2, which encodes T cell protein tyrosine phosphatase (TCPTP), have been linked with the development of several autoimmune diseases, including type 1 diabetes and Crohn’s disease. In this study, we have identified TCPTP as a key negative regulator of TCR signaling, which might explain the association of PTPN2 SNPs with autoimmune disease. We found that TCPTP dephosphorylates and inactivates Src family kinases to regulate T cell responses. Using T cell–specific TCPTP-deficient mice, we established that TCPTP attenuates T cell activation and proliferation in vitro and blunts antigen-induced responses in vivo. TCPTP deficiency lowered the in vivo threshold for TCR-dependent CD8+ T cell proliferation. Consistent with this, T cell–specific TCPTP-deficient mice developed widespread inflammation and autoimmunity that was transferable to wild-type recipient mice by CD8+ T cells alone. This autoimmunity was associated with increased serum levels of proinflammatory cytokines and anti-nuclear antibodies, T cell infiltrates in non-lymphoid tissues, and liver disease. These data indicate that TCPTP is a critical negative regulator of TCR signaling that sets the threshold for TCR-induced naive T cell responses to prevent autoimmune and inflammatory disorders arising.

The development of T cells in the thymus, the maintenance of a peripheral T cell repertoire, and the activation of T cells in secondary lymphoid organs rely on T cells recognizing antigen via the TCR. The MHC-restricted TCR complex comprises TCRα, -β, and -ζ subunits and three invariant CD3 polypeptides (γ, δ, ε) and can operate in conjunction with the CD4 or CD8 coreceptors (1). When the TCR engages its cognate peptide-MHC (pMHC) on antigen-presenting cells, the Src family protein tyrosine kinases (SFKs) Lck and Fyn are activated (1–3). CD4 and CD8 serve to enhance the recruitment of Lck to the TCR, but high-affinity ligands can signal independently of these coreceptors (3–5). Active SFKs phosphorylate TCRζ and CD3ε, allowing for the recruitment of the tyrosine kinase ZAP-70 (ζ chain–associated protein kinase of 70 kDa), which in turn is phosphorylated and activated by Lck to instigate effector cascades that promote gene expression, proliferation, and differentiation (1–3). The principal role of Lck in TCR signaling is highlighted by the severely disrupted thymocyte development and vastly reduced peripheral T cell numbers in Lck-deficient mice (6). Moreover, Lck is essential for naive T cell clonal expansion and the acquisition of effector functions in the periphery (2, 3, 7–9).

The duration and strength of the TCR signal propagated by Lck and ZAP-70 control T cell development in the thymus (2, 3). Thymocytes are selected based on their affinity for self-pMHC and the resulting intensity of TCR signaling (4, 10, 11); thymocytes with high-affinity TCRs that are capable of developing into autoreactive T cells undergo programmed cell death in a process known as negative selection, whereas those with low to moderate affinity develop further in a process known as positive selection (10). In the periphery, TCR recognition of foreign peptide antigen presented by MHC and the activation of Lck are essential in the initiation of naive T cell responses to invading pathogens, inducing clonal expansion, cytokine production, and the acquisition of effector functions (2, 3, 7–9). The affinity of the TCR for the presented foreign pMHC, the kinetics of the TCR-pMHC interaction, and the number of receptors engaged determine the strength of the TCR signal and the robustness of the T cell response (12–16). Productive T cell responses to foreign antigen are dependent on co-stimulation, the most common being that mediated by CD28 when it engages CD80/CD86 on activated antigen-presenting cells (1). Co-stimulation serves to quantitatively increase TCR/SFK signaling, allowing for the production of IL-2 and expression of the IL-2 receptor to promote T cell survival and to drive clonal expansion and effector development (1, 17).

Protein tyrosine phosphatases (PTPs) are important in T cell development and function and contribute to both the promotion and attenuation of T cell signaling. For example, the receptor type PTP CD45 is required for Lck activation and the promotion of TCR signaling (18–20). CD45 also regulates basal and TCR-instigated Lck Y394 autophosphorylation (21–23) and inhibits TCR signaling. Other PTPs have also been implicated in Lck Y394 dephosphorylation. Several lines of evidence point to SHP-1 being important in Lck inactivation, but conflicting studies suggest that SHP-1 does not suppress TCR-induced Lck activation and instead dephosphorylates LAT or ZAP-70 (24–27). LYP/PEP (encoded by PTPN22) has been shown to act directly on Lck Y394 in a cellular context (28), and TCR-induced Lck Y394 and ZAP-70 phosphorylation and downstream signaling and proliferation are elevated in effector/memory T cells from Ptpn22–/– mice (29). The importance of PTPs in regulating TCR signaling is underscored by the potential for human disease when PTP function is perturbed. For example, CD45 deficiency leads to severe combined immunodeficiency (30, 31), whereas a SNP in PTPN22 contributes to the development of autoimmune diseases, including type 1 diabetes, rheumatoid arthritis, systemic lupus erythematosus, and Graves disease (32).

PTPN2, encoding T cell PTP (TCPTP), has been identified as a susceptibility locus for autoimmune diseases. SNPs in PTPN2 have been linked to the development of type 1 diabetes, rheumatoid arthritis, and Crohn’s disease (33–35). Recently, the type 1 diabetes–linked PTPN2 variant rs1893217(C) has been associated with decreased PTPN2 expression in T cells (36). Deletion of the PTPN2 gene has also recently been implicated in the development of T cell acute lymphoblastic leukemias (37). Previous studies have shown that Ptpn2–/– mice develop symptoms of progressive systemic inflammatory disease by 1–2 weeks of age and die from severe anemia attributed to a defective bone microenvironment at 3–5 weeks of age (38, 39). However, the morbidity and mortality associated with global TCPTP deficiency preclude detailed analyses of T cell responses in Ptpn2–/– mice. Here we have conditionally deleted Ptpn2 in T cells and demonstrate that TCPTP attenuates TCR signaling and sets the threshold for T cell activation. Our studies provide insight into a key mechanism for T cell tuning for the prevention of immune and inflammatory disorders.

Generation of Lck-Cre;Ptpn2fl/fl mice.
We generated a floxed allele of Ptpn2 (loxP sites flanking exons 5 and 6 encoding the core of the catalytic domain including the catalytically essential Asp182 and Cys216 residues; Figure 1, A and B) by gene targeting in Bruce-4 embryonic stem cells and conditionally ablated TCPTP using the Lck-Cre transgene (40, 41). Floxing the Ptpn2 allele did not in itself affect TCPTP expression (data not shown). TCPTP expression was ablated in Lck-Cre;Ptpn2fl/fl thymocytes (CD4+CD8+, CD4+CD8–, CD4–CD8+) and peripheral CD4+ and CD8+ T cells (as assessed by immunoblot analysis using two different mAbs specific to the N [3E2; data not shown] and C termini [6F3] of TCPTP), but not in splenic CD19+ B cells, bone marrow–derived macrophages, or other tissues examined (data not shown, Figure 1C, and Supplemental Figure 1; supplemental material available online with this article; doi:
10.1172/JCI59492DS1). At 4–12 weeks of age, Lck-Cre;Ptpn2fl/fl mice appeared normal and healthy (data not shown).

Thymocyte development in Lck-Cre;Ptpn2fl/fl mice.
Ptpn2fl/fl and Lck-Cre;Ptpn2fl/fl thymocytes from 4-week-old mice were stained with fluorochrome-conjugated α-CD4, -CD8, -TCRβ, -CD69, and -CD5 and analyzed by flow cytometry. (A) Representative dot blots (numbers in outlined areas are percentages of cells in gate) and results from 3 experiments are shown. (B) Cells were gated for the different developmental stages (labeled 1–4) according to the expression of the positive selection markers CD69, CD5, and TCRβ, and absolute numbers were determined. Representative dot blots and results from 3 experiments are shown. (C) Thymocytes from OT-II TCR transgenic Ptpn2fl/fl (OT-II;Ptpn2fl/fl) and Lck-Cre;Ptpn2fl/fl (OT-II;Lck-Cre;Ptpn2fl/fl) mice were stained with fluorochrome-conjugated α-CD4 and α-CD8 and analyzed by flow cytometry. Cells were gated for the DP and CD4+SP stages, and absolute numbers and the indicated ratios were determined. Representative dot plots (numbers in outlined areas are percentages of cells in gate) and results from 2 independent experiments are shown. Results in A–C are mean ± SEM for the indicated numbers of mice; significance was determined using a 2-tailed Mann-Whitney U test; *P < 0.05, **P < 0.01, ***P < 0.001.

To further assess the impact of TCPTP deficiency on thymocyte development, we bred Ptpn2fl/fl and Lck-Cre;Ptpn2fl/fl mice onto OT-I and OT-II TCR transgenic backgrounds (43, 44). OT-II mice express a vα2/vβ5 TCR specific for the chicken OVA peptide 323ISQAVHAAHAEINEAGR339 (presented in the context of I-Ab class II MHC), whereas OT-I mice express a vα2/vβ5 TCR that is specific for the OVA peptide 257SIINEFKL264 (presented in the context of Kb class I MHC), selecting for CD4+SP and CD8+SP thymocytes, respectively (43, 44). Thymic cellularity in OT-II;Lck-Cre;Ptpn2fl/fl knockout mice was increased 2-fold when compared with littermate control OT-II;Ptpn2fl/fl mice (Figure 2C). This increase in cellularity was reflected by an increase in DP and CD4+SP thymocytes. Importantly, whereas DP cells were increased by less than 2-fold, the increase in CD4+SP thymocytes was more than 2-fold, translating into a significantly enhanced CD4+SP/DP ratio (Figure 2C); similar increases were noted when only clonotypic vα2hivβ5hi cells were assessed (Supplemental Figure 2B). Furthermore, the surface expression levels of TCRβ, CD69, and CD5 were increased in DP thymocytes (Supplemental Figure 2C), consistent with enhanced positive selection, and the numbers of thymocytes initiating (stage 2), undergoing (stage 3), and completing positive selection (stage 4) were also increased in OT-II Lck-Cre;Ptpn2fl/fl mice (Supplemental Figure 2D). In contrast, thymic cellularity and DP numbers were not altered in MHC class I–restricted OT-I Lck-Cre;Ptpn2fl/fl mice, but CD8+SP thymocytes were increased, albeit modestly (Supplemental Figure 2E). Moreover, negative selection — as assessed by the deletion of TCRvβ5+ CD4+CD8– thymocytes by endogenous superantigen mouse mammary tumor virus 9 (MMTV9; which can be presented by I-Ab; refs. 45, 46) (Supplemental Figure 4A); the induction of the negative selection marker Nur77 (ref. 47 and Supplemental Figure 4B); and the induction of apoptosis in DP thymocytes in response to anti-CD3ε (Supplemental Figure 4C) — was altered modestly, if at all. Taken together, these results are consistent with TCPTP deficiency promoting thymocyte positive selection without compromising negative selection.

T cell subsets in Lck-Cre;Ptpn2fl/fl mice.
In the LNs of 4- to 7-week-old Lck-Cre;Ptpn2fl/fl mice, the absolute numbers of CD4+ and CD8+ naive (CD62LhiCD44lo) T cells were increased (Figure 3 and Supplemental Figure 5), consistent with the elevated SP thymocyte development (Figure 2A). Naive T cells in spleen and liver were decreased in Lck-Cre;Ptpn2fl/fl mice, but this was accompanied by an increase in effector/memory (CD62LloCD44hi) T cells (Figure 3 and Supplemental Figure 5). No difference was evident in the homing of Lck-Cre;Ptpn2fl/fl naive CD8+ T cells to LN versus spleen after transfer into non-irradiated congenic Ly5.1 hosts (Supplemental Figure 6). The effector/memory phenotype in Lck-Cre;Ptpn2fl/fl mice was pronounced by 12 weeks of age, so that the total number of liver T cells was increased (Supplemental Figure 5). We found no overt differences in α-GalCer/CD1d tetramer+/TCRβ+ NKT cells, but moderate increases in CD4+FoxP3+CD25+ regulatory T cells in thymus, LNs, and spleen, but not liver, in 7- to 12-week-old mice (Supplemental Figure 7). These findings suggest that TCPTP deficiency results in the accumulation of peripheral T cells with an effector/memory phenotype.

TCPTP regulates SFKs but not ZAP-70 in T cells. Previously, we reported that SFKs can serve as bona fide substrates for TCPTP and that TCPTP dephosphorylates the Y418 activation loop autophosphorylation site (corresponding to Y394 in Lck and Y417 in Fyn) to inactivate SFKs (48). Lck and Fyn are the predominant SFKs expressed in thymocytes and T cells and are essential for T cell development and function (2, 3). Accordingly, we assessed TCPTP’s capacity to regulate T cell signaling by dephosphorylating and inactivating Lck and Fyn. As a first step, we determined whether Lck or Fyn could serve as TCPTP substrates. We took advantage of the TCPTP-D182A “substrate-trapping” mutant, which can form a stable complex with tyrosine phosphorylated substrates in a cellular context and protect such substrates from dephosphorylation by endogenous phosphatases (49–51). Human TCPTP or the TCPTP-D182A substrate-trapping mutant were coexpressed with wild-type Lck or the constitutively active Lck-Y505F mutant or with wild-type Fyn in COS1 cells, and phosphorylation of Lck and Fyn was monitored in cell lysates and TCPTP immunoprecipitates (Figure 4, a–c) using antibodies specific for Y418 phosphorylated SFKs. Expression of wild-type TCPTP ablated Lck and Fyn phosphorylation, whereas the TCPTP-D182A mutant enhanced Lck and Fyn phosphorylation, consistent with Lck and Fyn being direct substrates of TCPTP (Figure 4, a–c). As a control, we also assessed TCPTP’s capacity to recognize the Syk family PTK ZAP-70 as a substrate (Figure 4D). ZAP-70 activation is dependent on Lck-mediated phosphorylation at Y493 (52). Accordingly, ZAP-70 was coexpressed with and without limiting amounts of activated Lck in COS1 cells. In the absence of Lck, ZAP-70 was minimally phosphorylated at Y493 by endogenous SFKs. Wild-type 45-kDa TCPTP readily suppressed ZAP-70 Y493 phosphorylation mediated by either endogenous SFKs or overexpressed Lck, whereas the TCPTP-D182A substrate-trapping mutant did not alter ZAP-70 phosphorylation, but readily increased the Y394 phosphorylation status of cotransfected Lck (Figure 4D). These results are consistent with TCPTP regulating ZAP-70 phosphorylation via Lck. The results indicate that TCPTP has the capacity to recognize SFKs such as Lck and Fyn, but not ZAP-70, as direct substrates.

Lck and Fyn but not ZAP-70 can serve as TCPTP substrates. COS1 cells were transfected with vector control or constructs for 45-kDa TCPTP or TCPTP-D182A and (A and C) Lck or Lck-Y505F, (B) Fyn, or (D) ZAP-70. (A, B, and D) Cell lysates or (C) TCPTP immunoprecipitates were resolved by SDS-PAGE and immunoblotted for p-(Y418) SFK or p-(Y493) ZAP-70 and then reprobed as indicated. Lck species with retarded electrophoretic mobility resulting from TCPTP-D182A expression are indicated by arrows. (E–G) Jurkat E6.1 T cells transfected with vector control or constructs for TCPTP or TCPTP-D182A were stimulated by crosslinking with mouse α–human CD3ε at 37°C for the indicated times. (E and G) Cell lysates and (F) Lck immunoprecipitates were resolved by SDS-PAGE and immunoblotted for p-(Y418) SFK or antibodies specific for phosphorylated and activated ERK1/2 (p-ERK1/2) and reprobed as indicated. Retarded p-(Y418) SFK species indicative of Lck activation and p-ERK1 and p-ERK2 as well as the IgG heavy chain (IgGHC) are highlighted by arrows. Results shown are representative of 3 independent experiments.

Ptpn2 deletion enhances TCR signaling.
(A–D) MACS-purified (Miltenyi Biotec) CD8+SP thymocytes or (E) FACS-purified LN naive (CD44lo) CD8+ T cells or OT-I LN naive CD8+ T cells from Ptpn2fl/fl and Lck-Cre;Ptpn2fl/fl mice were stimulated with α-CD3ε at 37°C for the indicated times. Cell lysates or Lck immunoprecipitates were resolved by SDS-PAGE and immunoblotted for p-(Y418) SFK, p-(Y394) Lck, or p-ERK1/2 and then reprobed with actin as indicated. Retarded p-(Y418) SFK and p-(Y394) Lck species and p-ERK1 and p-ERK2 as well as IgGHC are indicated by arrows. Results shown are representative of at least 3 independent experiments. In A–C, electrophoretically retarded p-(Y418) SFK and p-(Y394) Lck species and p-ERK2 were quantified by densitometric analysis and normalized for actin or ERK2 as indicated. In A, data are shown as arbitrary units (AU). Quantified results are mean ± SEM for the indicated number of independent experiments; significance was determined using 2-tailed Mann-Whitney U test; *P < 0.05, **P < 0.01.

Deletion of Ptpn2 enhances TCR-dependent but not TCR-independent thymocyte proliferation. Our results indicate that TCPTP might be an important regulator of TCR-induced thymocyte signaling and responses. Accordingly, we assessed the impact of TCPTP deficiency on SP thymocyte proliferation. Proliferation was assessed in Ptpn2fl/fl versus Lck-Cre;Ptpn2fl/fl SP thymocytes in response to either TCR crosslinking with anti-CD3ε with/without anti-CD28, or stimulating with the phorbol ester PMA plus the calcium ionophore ionomycin, to promote TCR-dependent and -independent proliferation, respectively. TCPTP deficiency resulted in increased anti-CD3ε–induced thymocyte proliferation as monitored by [3H]thymidine incorporation (Figure 6A and Supplemental Figure 10A). The increased proliferation seen in response to anti-CD3ε stimulation alone in Lck-Cre;Ptpn2fl/fl thymocytes was similar to that achieved with anti-CD3ε plus anti-CD28 in Ptpn2fl/fl cells. Enhanced proliferation was observed in both CD8+SP and CD4+SP thymocytes as assessed by the dilution of CFSE, which measures division on a per-cell basis (Supplemental Figure 10B). In contrast, proliferation induced by PMA/ionomycin was not increased in Lck-Cre;Ptpn2fl/fl versus Ptpn2fl/fl thymocytes (Figure 6A). Thus, the increased proliferative capacity of TCPTP-deficient thymocytes may be specific to that induced by the TCR. Increased anti-CD3ε– but not PMA/ionomycin-induced proliferation was also evident in sorted CD8+SP Lck-Cre;Ptpn2fl/fl thymocytes (Figure 6A) and in sorted CD8+SP and CD4+SP thymocytes from 14-day-old Ptpn2–/– mice (ref. 38 and Supplemental Figure 10C). There was no overt difference in the proliferation of CD8+SP thymocytes from Lck-Cre;Ptpn2fl/+ heterozygous mice (Figure 6A). These results indicate that homozygous TCPTP deficiency enhances TCR-dependent, but not -independent, SP thymocyte proliferation.

Ptpn2 deletion enhances T cell proliferation in vivo. (A) FACS-purified CD8+ naive LN T cells from 4-week-old OT-I;Ptpn2fl/fl and OT-I;Lck-Cre;Ptpn2fl/fl mice were stained with CFSE and transferred into syngeneic hosts, which were immunized 24 hours later with vehicle control (PBS) or 2.5 μg SIINFEKL. Forty-eight hours after immunization LN, splenic, and liver T cells were isolated and stained with fluorochrome-conjugated antibodies against CD8 and TCRvα2 and CD8+ T cells analyzed by flow cytometry. Representative profiles (numbers are percentages of cells that have undergone >3 divisions) are shown; PBS controls are shown in black. Quantified results are mean ± SEM (pooled cells from 2 donors transferred into 5 recipients in each case) and are representative of 3 independent experiments; significance was determined using 2-tailed Mann-Whitney U test; *P < 0.05, **P < 0.01. (B) FACS-purified CD4+ naive LN T cells from 4 -week-old OT-II;Ptpn2fl/fl and OT-II;Lck-Cre;Ptpn2fl/fl mice were stained with CFSE and transferred into syngeneic hosts and 24 hours later immunized with OVA. Seventy-two hours after immunization, splenic T cells were isolated and stained with fluorochrome-conjugated antibodies against CD4 and TCRvα2 and CD4+ T cells analyzed by flow cytometry. Representative profiles (numbers are percentages of cells that have undergone >4 divisions) are shown. Quantified results are mean ± SEM (cells from 3 donors transferred into 2 recipients in each case and stimulated with 25 or 50 μg OVA) and are representative of 3 independent experiments; significance was determined using a 2-tailed Student’s t test; *P < 0.05.

Ptpn2 deletion enhances CD8+ T cell responses to low-affinity antigens.
Our findings indicate that TCPTP deficiency enhances TCR-instigated T cell activation and proliferation in vitro and in vivo. Moreover, our results suggest that TCPTP deficiency may permit CD8+ T cells to respond to antigen that may otherwise not be of high enough affinity to promote cellular division. A key advantage of the OT-I system is the availability of altered peptide ligands (APLs) based on N4 (Y3, Q4) for which TCR affinities and/or lytic or IFN-γ responses have been established (N4 > Y3 > Q4) (11, 14, 56). Accordingly, we compared the proliferation of Ptpn2fl/fl versus Lck-Cre;Ptpn2fl/fl naive OT-I CD8+ T cells stimulated with N4 versus APLs with lower TCR affinity. As a first step, we compared the proliferation of purified Ptpn2fl/fl versus Lck-Cre;Ptpn2fl/fl naive OT-I CD8 T cells in vitro in response to N4 versus Y3 and Q4 (Figure 9A). Since previous studies have established that responses induced by peptide presented by anchored class I MHC can be ascribed predominantly to eluted peptide self-presented by T cells (57, 58), we added peptides directly to the culture supernatant. Hommel et al. (58) have established that both TCR affinity and peptide antigen concentration dictate the response time, with lower affinity and concentration prolonging the time to first division. Therefore, we determined the impact of TCPTP deficiency on cell division by monitoring the dilution of CFSE to varying concentrations of N4, Y3, and Q4. TCPTP deficiency enhanced the responses to N4, Y3, and Q4, promoting cell division in a concentration-dependent manner. Importantly, the effects on cell division correlated with peptide affinity/responsiveness, with greater differences seen for Y3 and Q4 than N4 (Figure 9A).

Next, we determined whether TCPTP deficiency lowers the threshold for TCR-mediated proliferation in vivo. Previous studies have established that 4-fold-higher amounts of Y3 versus N4 are needed to induce a half-maximal IFN-γ response in OT-I T cells (14). Accordingly, we compared the proliferation of Ptpn2fl/fl and Lck-Cre;Ptpn2fl/fl adoptively transferred CFSE-labeled naive OT-I CD8+ T cells 3 days after injection of N4 versus Y3 (Figure 9B). In these experiments, naive OT-I CD8+ CFSE-labeled donor T cells from each mouse were transferred into two hosts and subsequently injected with N4 versus Y3, allowing for direct comparisons of responses. Only modest increases in proliferation were noted for N4 in Lck-Cre;Ptpn2fl/fl versus Ptpn2fl/fl transferred OT-I T cells 3 days after peptide administration (compare Figure 8A, where proliferation was assessed 2 days after peptide administration). In contrast, TCPTP deficiency significantly enhanced the proliferation of Lck-Cre;Ptpn2fl/fl OT-I T cells stimulated with Y3 (Figure 9B). Taken together, these findings are consistent with TCPTP deficiency lowering the threshold for TCR-instigated proliferation in vivo and allowing CD8+ T cells to respond to peptides with suboptimal TCR affinity.

Inflammation and autoimmunity in Lck-Cre;Ptpn2fl/fl mice.
One possible consequence of lowering the threshold for TCR-induced responses in Lck-Cre;Ptpn2fl/fl mice could be the development of immune and inflammatory disorders. We found that in 48-week-old aged Lck-Cre;Ptpn2fl/fl mice, circulating levels of the proinflammatory cytokines IL-6, TNF, and IFN-γ, as well as chemokines MIG and RANTES, previously associated with intrahepatic inflammation (59), were significantly elevated (Figure 10A). Furthermore, consistent with the development of inflammation, we found significant increases in CD4+ and CD8+ CD44hiCD62Llo effector/memory T cells in Lck-Cre;Ptpn2fl/fl LNs (resulting in increased LN weights; Supplemental Figure 13) and bone marrow, as well as lymphocytic infiltrates in non-lymphoid tissues such as liver and lung, associated with striking increases in CD44hiCD62Llo T cells (Figure 10, B, D, and E). Importantly, CD8+CD44hiCD62Llo T cells in the livers of aged mice were high for KLRG1 and low for CD127 (IL-7Rα) (Figure 10C), consistent with these being activated CD8+ effector T cells (60). In addition, TCPTP deficiency resulted in peanut agglutinin–positive germinal centers in the spleens of aged mice (Supplemental Figure 14) and high levels of anti-nuclear antibodies in sera (Figure 11A), indicative of a breakdown in tolerance. Indeed, aged Lck-Cre;Ptpn2fl/fl mice had significantly reduced body weights (Figure 11B), and 2 of 5 mice exhibited dermatitis and had to be culled by 10 months of age (data not shown). Moreover, hepatic lymphocytic infiltrates were accompanied by the development of fibrosis (assessed by staining with sirius red; Figure 11C) and overt liver damage as assessed by the presence of the hepatic enzymes alanine transaminase (ALT) and aspartate amino transferase (AST) in serum (Figure 11D). TCPTP expression was not altered in B220+ LN B cells, in splenic macrophages (Ly6G–/loCD11B+), granulocytes (Ly6GhiCD11B+) and dendritic cells (CD11c+) (Supplemental Figure 15), or in other tissues (data not shown) of aged Lck-Cre;Ptpn2fl/fl mice, consistent with the disease being a consequence of TCPTP deletion in T cells. Moreover, TCPTP deficiency did not alter the anti-CD3ε/IL-2–induced proliferation of regulatory T cells (CD4+CD25hi), nor did it affect their capacity to suppress the proliferation of naive (CD44loCD25lo) CD4+ T cells in response to anti-CD3ε (Supplemental Figure 16). Therefore, these results indicate that the development of disease in aged Lck-Cre;Ptpn2fl/fl mice could not be attributed to a defect in regulatory T cell function. Nonetheless, we performed additional experiments to establish whether the disease in Lck-Cre;Ptpn2fl/fl mice was T cell intrinsic/dependent. Total CD8+ T cells from the spleens of aged Ptpn2fl/fl and Lck-Cre;Ptpn2fl/fl mice (Supplemental Figure 17) were transferred into sublethally irradiated congenic hosts, and 12 weeks later, organ damage and serum anti-nuclear antibodies were assessed (Figure 11E and Supplemental Figure 17). We found that CD8+ T cells from Lck-Cre;Ptpn2fl/fl mice resulted in a significant increase in anti-nuclear antibodies and liver damage as monitored by the presence of serum ALT and AST (Figure 11E). Taken together, these results indicate that TCPTP deficiency in T cells results in a breakdown in tolerance and the development of autoimmunity.

TCR signaling affects the selection and survival of T cells at every stage of development (2, 3). In keeping with TCPTP being a key negative regulator of TCR signaling, we found that CD8+SP and CD4+SP thymocyte numbers were increased in Lck-Cre;Ptpn2fl/fl mice. In contrast, mice deficient for the phosphatases SHP-1 or PEP, which have been implicated in Lck dephosphorylation and inactivation, do not have any overt alterations in thymocyte subsets, unless placed on TCR transgenic backgrounds (29, 61). PEP-knockout mice on MHC class I– or II–restricted TCR transgenic backgrounds have enhanced positive but unaltered negative selection (29), whereas SHP-1 mutant (motheaten/motheaten) mice exhibit a dramatic decrease in DP numbers and a relative increase in CD4+SP thymocytes on an MHC class II–restricted TCR transgenic background, consistent with elevated negative and positive selection (61). In our studies, TCPTP deficiency increased positive selection but did not appear to alter negative selection. Importantly, TCPTP deficiency enhanced naive T cell responses to low-affinity ligands. Therefore, the selective effects of TCPTP deficiency on positive selection may be attributable to the enhanced responsivity of a subset of thymocytes with low affinity for self-pMHC. Similarly, differences in OT-I versus OT-II thymocyte responses to self-pMHC may be responsible for the contrasting effects of TCPTP deficiency on OT-I versus OT-II thymocyte development. However, we cannot exclude the possibility that additional pathways may be altered in Lck-Cre;Ptpn2fl/fl mice to affect thymocyte development. T cell–specific SOCS-1–deficient mice have increased CD8+SP, but not CD4+SP, thymocytes due to elevated IL-7–induced STAT5 signaling in DP thymocytes (62). STAT5 can serve as a TCPTP substrate (63, 64), and IL-2–induced STAT5 phosphorylation is increased in LN T cells from Ptpn2–/– mice that are globally deficient for TCPTP (64). It is possible that elevated cytokine signaling may have in part contributed to the effects of TCPTP deficiency on CD8+SP thymocyte development. On the other hand, the increased CD4+SP thymocyte development may have been due to elevated TCR signaling alone, since high levels of SFK activation favor the development of CD4+SP thymocytes (65, 66).

In the periphery, TCPTP deficiency resulted in a memory phenotype. The number of T cells with an effector/memory phenotype increased progressively from 4 to 12 weeks of age, and this was accompanied by a decrease in naive T cell numbers. Early in life, the peripheral T cell pool consists largely of naive T cells, but with age and thymic atrophy, this shifts to a predominance of memory T cells (67). Memory T cells are generated after an immune challenge and the exposure of naive T cells to foreign antigen. However, naive T cell homeostasis and lymphopenia-induced proliferation (LIP) can also result in the generation of “memory phenotype” cells, and these cells have many of the characteristics of true memory T cells (67). The generation of memory phenotype T cells is dependent on naive T cell TCR interaction with low-affinity self-pMHC plus interaction with γc cytokines (67). The rate of naive T cell LIP relies on TCR affinity for self-pMHC; T cells with high-affinity TCRs proliferate faster than T cells with low-affinity TCRs (68, 69). Thus, an overall consequence of LIP is the selection of high-affinity, potentially self-reactive T cells. One possibility is that the memory phenotype and the decline in the naive T cell pool in Lck-Cre;Ptpn2fl/fl mice may have been attributable to the conversion of naive T cells to memory phenotype T cells due to enhanced T cell homeostasis/LIP. Moreover, by lowering the threshold for TCR responses, TCPTP deficiency might render CD8+ T cells with low affinity for self-pMHC as “high-affinity” T cells with an increased propensity for overt autoreactivity and disease. Thus, enhanced T cell homeostasis/LIP may also account for the development of autoimmune disease in Lck-Cre;Ptpn2fl/fl mice. This would be in keeping with the previously established potential of lymphopenia to contribute to the development of autoimmune diseases, such as type 1 diabetes, rheumatoid arthritis, Crohn’s disease, and systemic lupus erythematosus (70).

It is important to note that the autoimmune phenotype in Lck-Cre;Ptpn2fl/fl mice was evident on a “non-autoimmune” C57BL/6 strain background. Autoimmunity occurred despite the increased number of regulatory T cells and was not associated with a defect in regulatory T cell function. A SNP in PTPN22 (encodes LYP/PEP) contributes to the development of several autoimmune diseases, including type 1 diabetes, rheumatoid arthritis, and lupus (32). However, in contrast to Lck-Cre;Ptpn2fl/fl mice, PEP–/– mice do not develop inflammation and organ damage on a C57BL/6 background (29). Our studies indicate that TCPTP is an important negative regulator of TCR and SFK signaling in naive T cells. In contrast, PEP is redundant in naive T cells and functions to dephosphorylate and inactivate Lck in effector/memory T cells (29). TCPTP’s regulation of TCR/SFK signaling in naive T cells may be key to the onset of autoimmunity in Lck-Cre;Ptpn2fl/fl mice. However, TCPTP has also been implicated in the regulation of JAK/STAT (64) and TNF signaling (48), and we cannot exclude the possibility that enhanced cytokine signaling may also contribute to disease progression. Indeed, IL-2–induced STAT5 signaling and responses were increased in TCPTP-deficient CD4+ and CD8+ T cells. Although STAT5 can serve as a TCPTP substrate (63), the enhanced IL-2–induced responses were most likely due to elevated TCR-induced expression of the IL-2 receptor. STAT6 can also serve as a TCPTP substrate (71), but we found no overt difference in IL-4–induced STAT6 signaling and responses in CD4+ T cells in vitro. Additional studies are needed to specifically determine the contributions of potentially altered cytokine signaling in Lck-Cre;Ptpn2fl/fl mice. Interestingly, TCPTP differentially contributed to naive CD4+ versus CD8+ T cell responses. TCR-induced activation and proliferation were enhanced in both CD4+ and CD8+Lck-Cre;Ptpn2fl/fl T cells, but TCR threshold responses were only evident in CD8+ T cells. This may been due to TCPTP differentially contributing to the regulation of Lck and Fyn, or possibly other substrates in CD4+ versus CD8+ T cells. Furthermore, our studies do not exclude the possibility that additional PTPs contribute to the regulation of SFKs in naive T cells. Indeed, we suggest that TCPTP regulates responses to low-affinity antigens and that other PTPs may have a more prominent role in regulating TCR signaling/responses to high-affinity or foreign antigens (since CD8+ proliferation induced by saturating concentrations of crosslinking antibody, co-stimulation, or high-affinity peptide antigen were modestly affected by TCPTP deficiency). One possible candidate is SHP-1, which dephosphorylates Lck, ZAP-70, and LAT (24, 26, 27) and has recently been show to regulate the magnitude of a primary CD8+ T cell response (72).

The TCR proximal SFKs Lck and Fyn are essential for T cell immunity and naive T cell homeostasis (2, 3, 8, 9, 73). Conversely, sustained Lck activation can result in a loss of tolerance and the onset of disease (3, 74). We propose that elevated TCR-induced SFK activation in TCPTP-deficient T cells may be responsible for the inflammatory and autoimmune phenotype in Lck-Cre;Ptpn2fl/fl mice. In humans, genome-wide association studies have linked PTPN2 SNPs to autoimmune disorders (33–35), whereas the type 1 diabetes–associated PTPN2 variant rs1893217(C) has been linked to a decrease in PTPN2 message in CD4+CD45RO+ T cells (36). Although STAT5 can serve as a substrate for TCPTP (63), surprisingly the decreased PTPN2 expression in the type 1 diabetes variant has been associated with decreased IL-2–induced STAT5 signaling (36). Although the molecular basis for this apparent defect in STAT5 signaling remains unclear (36), a possible consequence may be perturbations in the development/homeostasis of regulatory T cells that prevent autoimmunity (17). In this study, we delineate an alternate mechanism whereby TCPTP deficiency may contribute to the breakdown of immunological tolerance. Our studies highlight TCPTP’s role in T cell development and function and establish its capacity to set the threshold for TCR-induced responses for the prevention of autoimmune and inflammatory diseases.

Mice. We maintained mice on a 12-hour light/12-hour dark cycle in a temperature-controlled high barrier facility with free access to food and water. We used aged-matched and, where indicated, sex-matched mice for all experiments. Ptpn2–/– mice on a 129/Sv × BALB/c mixed background (38) were backcrossed onto a BALB/c background for 8 generations. Ptpn2–/– mice were genotyped as described previously (38). The Lck-Cre (originating from James D. Marth’s laboratory, UCSD, La Jolla, California, USA; refs. 40, 41) and TCR (OT-I and OT-II) transgenic mice on C57BL/6J backgrounds were gifts from W. Alexander and W. Heath (Walter and Eliza Hall Institute).

Ptpn2fl/+ mice.
We used a 129/SvJ mouse BAC genomic library clone (pBeloBAC11, Incyte Genomics) for the generation of a targeting construct (75) that incorporated loxP sites flanking exons (ex) 5 and 6 and a neomycin resistance cassette flanked by FRT sites (Figure 1). The linearized targeting construct was electroporated into Bruce-4 (C57BL/6J) ES cells, and correctly targeted clones were injected into BALB/c blastocysts. High-percentage male chimeras were mated with C57BL/6J mice to produce Ptpn2fl/+ offspring and subsequently with FLPe mice (C57BL/6) to excise the neomycin resistance cassette (75). Ptpn2fl/+ mice were mated with Lck-Cre mice for the conditional ablation of TCPTP in T cells. PCR was used to monitor for the floxed allele and the Cre transgene (75). Tissues of experimental mice were analyzed by immunoblotting for TCPTP expression. TCPTP was effectively deleted in thymocytes and T cells in more than 90% of cases, and only mice with less than 90% TCPTP deletion were used for the indicated analyses; TCPTP deletion was not evident in other tissues, including B cells, macrophages, monocytes, granulocytes, dendritic cells, spleen, kidney, pancreas, muscle, liver, heart, brain, lung, adipose tissue, salivary gland, and tail (Figure 1, Supplemental Figures 1 and 15).

Flow cytometry. Single-cell suspensions from freshly dissected thymi, spleens, and LNs were obtained by gently compressing samples between frosted glass slides and washing with cold PBS supplemented with 0.2% (w/v) BSA or 2% (v/v) FBS (CSL); thymocytes were homogenized further with an 18G needle. The resulting cell suspensions were recovered by centrifugation (330 g, 5 minutes at 4°C) and cell counts determined using a Z2 Coulter Counter (Beckman Coulter). Hepatic lymphocytes were isolated from perfused livers cut it into small pieces and strained through a 200-μm sieve. Hepatocytes and cell debris were removed using a 33% Percoll (GE Healthcare) gradient at room temperature. Red blood cells were removed using red blood cell lysing buffer (Sigma-Aldrich).

T cell isolation. Naive (CD44lo) CD8+ T cells used for TCR signaling and proliferation assays were purified from pooled LNs by FACS with an Influx Sorter (BD Biosciences). DP and CD8+SP thymocytes were also purified by FACS. Naive CD8+ T cells and DP thymocytes were routinely tested for purity (>99%). The purity for FACS-purified CD8+SP thymocytes was greater than 95%.

For assessment of TCR signaling in CD8+SP thymocytes, cells were purified using an autoMACS (Miltenyi Biotec). In brief, thymocytes were incubated with α-CD4–PE, followed by the addition of α-PE–conjugated MicroBeads. CD4+SP and DP thymocytes were depleted, and the fraction containing DN and CD8+SP thymocytes was labeled with α-CD8–PE, followed by incubation with α-PE–conjugated MicroBeads. CD8+SP thymocytes were obtained using the autoMACS positive selection program. The purity of CD8+SP cells was 88%–93%; contamination with CD4+SP and DP thymocytes was less than 1% and that of DN thymocytes was 6%–12%.

Plasmids. pMT2, TCPTP-pMT2, and TCPTP-D182A-pMT2 constructs have been described previously (50). Lck-pJ3Ω and Lck-Y505F-pJ3Ω were generated by PCR using Platinum Pfx DNA Polymerase (Invitrogen) and Lck-pEF/HA and Lck-Y505F-pEF/HA as templates, respectively. For cloning the human wild-type and mutant Lck cDNAs into pJ3Ω, the oligonucleotides incorporated a HindIII site immediately 5′ to the initiating codon (5′-CGCCGCAAGCTTATGGGCTGTGGCTGCAGCTCA-3′) and a KpnI site immediately 3′ to the terminating codon (5′-CGCCGCGGTACCTCAAGGCTGAGGCTGGTACTGG-3′). The HindIII/KpnI-digested PCR products were cloned into the HindIII/KpnI sites of pJ3Ω.

Substrate trapping. COS1 cells and Jurkat E6.1 T cells were cultured at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s and RPMI-1640 medium, respectively, containing 5% (v/v) FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin. Cells were transfected as indicated by electroporation (transfection efficiencies of approximately 75%–90% for COS1 and approximately 70% for Jurkat T cells) as described previously (50). After 48 hours, cells were lysed in substrate-trapping lysis buffer and precleared with Pansorbin (Calbiochem), and cell lysates or TCPTP immunoprecipitates (CF4) were processed as described previously (50).

Cytokine detection. Serum cytokines from 48-week-old mice were detected with the BD Cytometric Bead Array kit according to the manufacturer’s instructions (BD Biosciences).

Histology. Lung and liver tissue from 40- and 48-week-old mice were fixed with formalin and embedded in paraffin. Tissue sections were stained with hematoxylin, followed by eosin counterstaining. Sections were analyzed using a BX51 Olympus slide system and OlyVIA imaging software (Olympus).

Statistics. Statistical analyses were performed using GraphPad Prism software and the nonparametric, unpaired, 2-tailed Mann-Whitney U test, where n ≥ 4, and an unpaired, 2-tailed Student’s t test, where n = 3. P values less than 0.05 were considered significant.

Study approval. All experiments were performed in accordance with the National Health and Medical Research Council (NHMRC) Australian Code of Practice for the Care and Use of Animals. All protocols were approved by the Monash University School of Biomedical Sciences Animal Ethics Committee.

We thank A. Strasser, W. Langdon, F. Carbone, W. Heath, and S. Turner for helpful discussions. This work was supported by the NHMRC of Australia (to T. Tiganis, D.I. Godfrey, and S.M. Russell); S.M. Russell is an Australian Research Council Future Fellow, and T. Tiganis and D.I. Godfrey are NHMRC Principal Research Fellows.